Erythroid clean

Parameter settings

Import Seurat object

Subset by treatment group

Normalize, Scale and Dim reduction of replicate groups

FACS sort overlap

Sort out cells which overlap FACS sort in low frequncy (N<=2)

clov: cluster overlap
clpu: cluster pure
clmi: cluster mixed

Find DEG in cluster with mixed Myeloid / Progenitor population

NaCl Myeloid cells mixed in Progenitor dominant cluster

NaCl Progenitor cells mixed in Myeloid dominant cluster

CpG Myeloid cells mixed in Progenitor dominant cluster

Cpg Progenitor cells mixed in Myeloid dominant cluster

Remove cells by cluster and marker genes

B-cell cluster

Plasmablast: Can proliferate, short half-life, high number of mitochondria, low level of B220
Plasma cells cannot switch antibody classes, cannot act as antigen-presenting cells because they no longer display MHC-II, and do not take up antigen because they no longer display significant quantities of immunoglobulin on the cell surface

CpG: Cluster 17
NaCl: Cluster 17

Plasma cells and plasmablast can be present in the B220- gate which coexpress taci (Tnfrsf13b) and Cd138 (Sdc1) respectively. However, Tnfrsf13b is also expressed by plasmacytoid dendritic cells

Igkc - Immunoglobulin kappa constant (light chain)
Iglc - Immunoglobulin lambda constant (light chain)

Plasmablast cell Tnfrsf13b expression vs heavy and light constant chain

Plasma cell Tnfrsf13b expression vs heavy and light constant chain

Remove

T-Cell cluster

Trac - T cell receptor alpha constant
Trbc1 - T cell receptor beta constant 1
Trbc2 - T cell receptor beta constant 2
Trdc - T cell receptor delta constant
Trgc1 - T cell receptor gamma constant 1
Trgc2 - T cell receptor gamma constant 2

Cd247 - T-cell surface glycoprotein Cd3 zeta chain (Cd3z)
Cd3g - T-cell surface glycoprotein Cd3 gamma chain
Cd3e - T-cell surface glycoprotein Cd3 epsilon chain
Cd3d - T-cell surface glycoprotein Cd3 delta chain

Check Myeloid Hb contamination

Those might be myeloid cells which phagocytosed

Recompute dimensional reduction

Compute on merged data

Save output

Session info